diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 40 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38364191f..4a636f6e86 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -76,6 +76,7 @@ #:use-module (gnu packages code) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages cpio) #:use-module (gnu packages cran) #:use-module (gnu packages crates-io) @@ -7103,23 +7104,49 @@ of these reads to align data quickly through a hash-based indexing scheme.") (define-public sortmerna (package (name "sortmerna") - (version "2.1b") + (version "4.3.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/biocore/sortmerna") - (commit version))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf")))) - (build-system gnu-build-system) + "0f8jfc8vsq6llhbb92p9yv7nbp566yqwfcmq3g2hw0n7d8hyl3a8")))) + (build-system cmake-build-system) (outputs '("out" ;for binaries "db")) ;for sequence databases (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:tests? #false ;unclear how to run them + #:configure-flags + #~(list "-DWITH_TESTS=ON" + "-DCMAKE_CXX_FLAGS=-pthread" + "-DZLIB_STATIC=OFF" + "-DROCKSDB_STATIC=OFF" + "-DPORTABLE=OFF" ;do not use static linking + (string-append "-DROCKSDB_HOME=" + #$(this-package-input "rocksdb")) + (string-append "-DRAPIDJSON_HOME=" + #$(this-package-input "rapidjson")) + (string-append "-DRapidJson_DIR=" + #$(this-package-input "rapidjson") + "/lib/cmake/RapidJSON") + (string-append "-DRapidJSON_INCLUDE_DIR=" + #$(this-package-input "rapidjson") + "/include")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'find-concurrentqueue-headers + (lambda* (#:key inputs #:allow-other-keys) + ;; Ensure that headers can be found + (setenv "CPLUS_INCLUDE_PATH" + (string-append (search-input-directory + inputs "/include/concurrentqueue") + ":" + (or (getenv "CPLUS_INCLUDE_PATH") ""))))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -7127,14 +7154,16 @@ of these reads to align data quickly through a hash-based indexing scheme.") (db (assoc-ref outputs "db")) (share (string-append db "/share/sortmerna/rRNA_databases"))) - (install-file "sortmerna" bin) - (install-file "indexdb_rna" bin) + (install-file "src/sortmerna" bin) (for-each (lambda (file) (install-file file share)) - (find-files "rRNA_databases" ".*fasta")) - #t)))))) + (find-files "../source/data/rRNA_databases" ".*fasta")))))))) (inputs - (list zlib)) + (list concurrentqueue + gflags ; because of rocksdb + rapidjson rocksdb zlib)) + (native-inputs + (list pkg-config)) (home-page "https://bioinfo.lifl.fr/RNA/sortmerna/") (synopsis "Biological sequence analysis tool for NGS reads") (description |